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Yorodumi- EMDB-18780: Single particle cryo-EM co-structure of E. coli AcrB with bound B... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18780 | |||||||||
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Title | Single particle cryo-EM co-structure of E. coli AcrB with bound BDM91531 inhibitor | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Efflux Pump Inhibitor / Transmembrane Binding / Antibiotic Resistance / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information alkane transmembrane transporter activity / alkane transport / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / enterobactin transport / enterobactin transmembrane transporter activity / periplasmic side of plasma membrane / bile acid transmembrane transporter activity / bile acid and bile salt transport / xenobiotic transport ...alkane transmembrane transporter activity / alkane transport / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / enterobactin transport / enterobactin transmembrane transporter activity / periplasmic side of plasma membrane / bile acid transmembrane transporter activity / bile acid and bile salt transport / xenobiotic transport / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / fatty acid transport / response to toxic substance / response to xenobiotic stimulus / response to antibiotic / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.23 Å | |||||||||
Authors | Boernsen C / Mueller RT / Pos KM / Frangakis AS | |||||||||
Funding support | Germany, France, 2 items
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Citation | Journal: To be published Title: Single particle cryo-EM co-structure of E. coli AcrB with bound BDM91531 inhibitor at 3.23 A resolution Authors: Boernsen C / Mueller RT | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18780.map.gz | 53.3 MB | EMDB map data format | |
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Header (meta data) | emd-18780-v30.xml emd-18780.xml | 17.3 KB 17.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18780_fsc.xml | 10.5 KB | Display | FSC data file |
Images | emd_18780.png | 130.4 KB | ||
Filedesc metadata | emd-18780.cif.gz | 6.3 KB | ||
Others | emd_18780_half_map_1.map.gz emd_18780_half_map_2.map.gz | 95.5 MB 95.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18780 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18780 | HTTPS FTP |
-Validation report
Summary document | emd_18780_validation.pdf.gz | 1.3 MB | Display | EMDB validaton report |
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Full document | emd_18780_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | emd_18780_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | emd_18780_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18780 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18780 | HTTPS FTP |
-Related structure data
Related structure data | 8qzqMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_18780.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_18780_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_18780_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Trimeric E. coli AcrB with bound BDM91531 efflux pump inhibitor
Entire | Name: Trimeric E. coli AcrB with bound BDM91531 efflux pump inhibitor |
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Components |
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-Supramolecule #1: Trimeric E. coli AcrB with bound BDM91531 efflux pump inhibitor
Supramolecule | Name: Trimeric E. coli AcrB with bound BDM91531 efflux pump inhibitor type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) / Strain: K12 |
-Macromolecule #1: Multidrug efflux pump subunit AcrB
Macromolecule | Name: Multidrug efflux pump subunit AcrB / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) / Strain: K-12 |
Molecular weight | Theoretical: 113.66518 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MPNFFIDRPI FAWVIAIIIM LAGGLAILKL PVAQYPTIAP PAVTISASYP GADAKTVQDT VTQVIEQNMN GIDNLMYMSS NSDSTGTVQ ITLTFESGTD ADIAQVQVQN KLQLAMPLLP QEVQQQGVSV EKSSSSFLMV VGVINTDGTM TQEDISDYVA A NMKDAISR ...String: MPNFFIDRPI FAWVIAIIIM LAGGLAILKL PVAQYPTIAP PAVTISASYP GADAKTVQDT VTQVIEQNMN GIDNLMYMSS NSDSTGTVQ ITLTFESGTD ADIAQVQVQN KLQLAMPLLP QEVQQQGVSV EKSSSSFLMV VGVINTDGTM TQEDISDYVA A NMKDAISR TSGVGDVQLF GSQYAMRIWM NPNELNKFQL TPVDVITAIK AQNAQVAAGQ LGGTPPVKGQ QLNASIIAQT RL TSTEEFG KILLKVNQDG SRVLLRDVAK IELGGENYDI IAEFNGQPAS GLGIKLATGA NALDTAAAIR AELAKMEPFF PSG LKIVYP YDTTPFVKIS IHEVVKTLVE AIILVFLVMY LFLQNFRATL IPTIAVPVVL LGTFAVLAAF GFSINTLTMF GMVL AIGLL VDDAIVVVEN VERVMAEEGL PPKEATRKSM GQIQGALVGI AMVLSAVFVP MAFFGGSTGA IYRQFSITIV SAMAL SVLV ALILTPALCA TMLKPIAKGD HGEGKKGFFG WFNRMFEKST HHYTDSVGGI LRSTGRYLVL YLIIVVGMAY LFVRLP SSF LPDEDQGVFM TMVQLPAGAT QERTQKVLNE VTHYYLTKEK NNVESVFAVN GFGFAGRGQN TGIAFVSLKD WADRPGE EN KVEAITMRAT RAFSQIKDAM VFAFNLPAIV ELGTATGFDF ELIDQAGLGH EKLTQARNQL LAEAAKHPDM LTSVRPNG L EDTPQFKIDI DQEKAQALGV SINDINTTLG AAWGGSYVND FIDRGRVKKV YVMSEAKYRM LPDDIGDWYV RAADGQMVP FSAFSSSRWE YGSPRLERYN GLPSMEILGQ AAPGKSTGEA MELMEQLASK LPTGVGYDWT GMSYQERLSG NQAPSLYAIS LIVVFLCLA ALYESWSIPF SVMLVVPLGV IGALLAATFR GLTNDVYFQV GLLTTIGLSA KNAILIVEFA KDLMDKEGKG L IEATLDAV RMRLRPILMT SLAFILGVMP LVISTGAGSG AQNAVGTGVM GGMVTATVLA IFFVPVFFVV VRRRFSRKNE DI EHSHTVD HH UniProtKB: Multidrug efflux pump subunit AcrB |
-Macromolecule #2: [3-(3-chloranyl-2-piperazin-1-yl-quinolin-6-yl)phenyl]methanamine
Macromolecule | Name: [3-(3-chloranyl-2-piperazin-1-yl-quinolin-6-yl)phenyl]methanamine type: ligand / ID: 2 / Number of copies: 1 / Formula: XE9 |
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Molecular weight | Theoretical: 352.861 Da |
-Macromolecule #3: [(2~{R})-1-[[(2~{R})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphory...
Macromolecule | Name: [(2~{R})-1-[[(2~{R})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-3-undecanoyloxy-propan-2-yl] tricosanoate type: ligand / ID: 3 / Number of copies: 1 / Formula: WR6 |
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Molecular weight | Theoretical: 751.023 Da |
Chemical component information | ChemComp-WR6: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.2 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum SE / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2597 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 3.5 µm / Calibrated defocus min: 0.8 µm / Calibrated magnification: 130000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-8qzq: |